This is not Skerry specific as it applies to all trailers.  You should position the boat so that the trailer tongue weight is 10-15% of the total weight of the trailer.  If you have too little tongue weight, the trailer will sway side to side at highway speeds.  For really light rigs like yours (and mine), even more tongue weight is just fine as long as your tow rig is rated for it.

I wound up setting my axle further back than the Trailex assembly instructions for the same reasons, it's a light load and needed to keep load on the hitch.  My axle is about 137 inches from the hitch.  I also set the bow prop a bit farther back because there's a fair bow overhang and didn't want it too close to the corners of the car when making a sharp turn.  It wound up about 28" behind the hitch.

   Mummihog, do you have some sort of eyebolt on the stem to snug up the boat when you're trailering? Any advice?

   I cartopped my skerry until this last year.  I didn't build mine with any reinforcement for an eyebolt, but I did have a nice stainless cleat I put on the breast hook that I use for anchor rode or painters, and it serves as a tiedown point for a line to the front of the trailer. A line runs through the open base of the cleat, down and through the aluminum tongue skid and back up through a purchase loop or cam cleat.